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Xue H, Guo Q, Yu A, Lin M, Chen X, Xu L. Genetic analysis of chorionic villus tissues in early missed abortions. Sci Rep 2023; 13:21719. [PMID: 38081877 PMCID: PMC10713591 DOI: 10.1038/s41598-023-48358-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
Chromosomal abnormalities are the most common etiology of early spontaneous miscarriage. However, traditional karyotyping of chorionic villus samples (CVSs) is limited by cell culture and its low resolution. The objective of our study was to investigate the efficiency of molecular karyotyping technology for genetic diagnosis of early missed abortion tissues. Chromosome analysis of 1191 abortion CVSs in early pregnancy was conducted from August 2016 to June 2021; 463 cases were conducted via copy-number variations sequencing (CNV-seq)/quantitative fluorescent-polymerase chain reaction (QF-PCR) and 728 cases were conducted using SNP array. Clinically significant CNVs of CVSs were identified to clarify the cause of miscarriage and to guide the couples' subsequent pregnancies. Among these, 31 cases with significant maternal cell contamination were removed from the study. Among the remaining 1160 samples, 751 cases (64.7%) with genetic abnormalities were identified, of which, 531 (45.8%) were single aneuploidies, 31 (2.7%) were multiple aneuploidies, 50 (4.3%) were polyploidies, 54 (4.7%) were partial aneuploidies, 77 (6.6%) had submicroscopic CNVs (including 25 with clinically significant CNVs and 52 had variants of uncertain significance), and 8 cases (0.7%) were uniparental disomies. Our study suggests that both SNP array and CNV-seq/QF-PCR are reliable, robust, and high-resolution technologies for genetic diagnosis of miscarriage.
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Affiliation(s)
- Huili Xue
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Gulou District, No. 18 Daoshan Road, Fuzhou, 350001, Fujian, China.
| | - Qun Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Gulou District, No. 18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Aili Yu
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Gulou District, No. 18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Min Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Gulou District, No. 18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Gulou District, No. 18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Gulou District, No. 18 Daoshan Road, Fuzhou, 350001, Fujian, China.
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Kikas T, Punab AM, Kasak L, Poolamets O, Vihljajev V, Pomm K, Reiman M, Tjagur S, Korrovits P, Punab M, Laan M. Microdeletions and microduplications linked to severe congenital disorders in infertile men. Sci Rep 2023; 13:574. [PMID: 36631630 DOI: 10.1038/s41598-023-27750-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Data on the clinical validity of DNA copy number variants (CNVs) in spermatogenic failure (SPGF) is limited. This study analyzed the genome-wide CNV profile in 215 men with idiopathic SPGF and 62 normozoospermic fertile men, recruited at the Andrology Clinic, Tartu University Hospital, Estonia. A two-fold higher representation of > 1 Mb CNVs was observed in men with SPGF (13%, n = 28) compared to controls (6.5%, n = 4). Seven patients with SPGF were identified as carriers of microdeletions (1q21.1; 2.4 Mb) or microduplications (3p26.3, 1.1 Mb; 7p22.3-p22.2, 1.56 Mb; 10q11.22, 1.42 Mb, three cases; Xp22.33; 2.3 Mb) linked to severe congenital conditions. Large autosomal CNV carriers had oligozoospermia, reduced or low-normal bitesticular volume (22-28 ml). The 7p22.3-p22.2 microduplication carrier presented mild intellectual disability, neuropsychiatric problems, and short stature. The Xp22.33 duplication at the PAR1/non-PAR boundary, previously linked to uterine agenesis, was detected in a patient with non-obstructive azoospermia. A novel recurrent intragenic deletion in testis-specific LRRC69 was significantly overrepresented in patients with SPGF compared to the general population (3.3% vs. 0.85%; χ2 test, OR = 3.9 [95% CI 1.8-8.4], P = 0.0001). Assessment of clinically valid CNVs in patients with SPGF will improve their management and counselling for general and reproductive health, including risk of miscarriage and congenital disorders in future offspring.
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Zhu S, Lin D, Ye Z, Chen X, Jiang W, Xu H, Quan S, Zheng B. GOLPH3 modulates expression and alternative splicing of transcription factors associated with endometrial decidualization in human endometrial stromal cells. PeerJ 2023; 11:e15048. [PMID: 36967990 PMCID: PMC10035422 DOI: 10.7717/peerj.15048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/21/2023] [Indexed: 03/29/2023] Open
Abstract
Endometrial decidualization is a decidual tissue formed by the proliferation and re-differentiation of endometrial stroma stimulated by decidualization inducing factors. It is very important for the proper maintenance of pregnancy. Previous studies speculated that Golgi phosphoprotein 3 (GOLPH3) may have a regulatory role in the process of endometrial decidualization, while the specific molecular mechanisms of GOLPH3 is unclear. In this part, GOLPH3 was silenced in human endometrial stromal cells (hESCs), and the transcriptome data (RNA-seq) by GOLPH3 knockdown (siGOLPH3) was obtained by high-throughput sequencing technology so as to analyze the potential targets of GOLPH3 at expression and alternative splicing levels in hESCs. Through bioinformatics analysis, we found that siGOLPH3 can significantly affect the overall transcriptional level of hESCs. A total of 6,025 differentially expressed genes (DEGs) and 4,131 differentially alternative splicing events (DASEs) were identified. Through functional cluster analysis of these DEGs and genes where differential alternative splicing events are located, it is found that they are enriched in the PI3K/Akt signaling pathway, RNA splicing and processing, transcription factors and other pathways related to endometrial decidualization and important biological processes, indicating the important biological function of GOLPH3. At the same time, we focused on the analysis of the transcription factors regulated by GOLPH3, including gene expression regulation and the regulation of variable splicing. We found that GOLPH3can regulate the expression of transcription factors such as LD1, FOSL2, GATA2, CSDC2 and CREB3L1. At the same time, it affects the variable splicing mode of FOXM1 and TCF3. The function of these transcription factors is directly related to decidualization of endometrium. Therefore, we infer that GOLPH3 may participate in endometrial de membrane by regulating expression and alternative splicing levels of transcription factors. We further identified the role of GOLPH3 in the transcriptional mechanism. At the same time, it also expands the function mode of GOLPH3 protein molecule, and provides a theoretical basis for downstream targeted drug research and development and clinical application.
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Affiliation(s)
- Suqin Zhu
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
| | - Dianliang Lin
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
| | - Zhoujie Ye
- Medical Research Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
| | - Xiaojing Chen
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
| | - Wenwen Jiang
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
| | - Huiling Xu
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
| | - Song Quan
- Department of Obstetrics and Gynecology, Southern Medical University, Guangzhou, Guangdong, China
| | - Beihong Zheng
- Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian, China
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Shilton CA, Kahler A, Roach JM, Raudsepp T, de Mestre AM. Lethal variants of equine pregnancy: is it the placenta or foetus leading the conceptus in the wrong direction? Reprod Fertil Dev 2022; 35:51-69. [PMID: 36592981 DOI: 10.1071/rd22239] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Embryonic and foetal loss remain one of the greatest challenges in equine reproductive health with 5-10% of established day 15 pregnancies and a further 5-10% of day 70 pregnancies failing to produce a viable foal. The underlying reason for these losses is variable but ultimately most cases will be attributed to pathologies of the environment of the developing embryo and later foetus, or a defect intrinsic to the embryo itself that leads to lethality at any stage of gestation right up to birth. Historically, much research has focused on the maternal endometrium, endocrine and immune responses in pregnancy and pregnancy loss, as well as infectious agents such as pathogens, and until recently very little was known about the both small and large genetic variants associated with reduced foetal viability in the horse. In this review, we first introduce key aspects of equine placental and foetal development. We then discuss incidence, risk factors and causes of pregnancy loss, with the latter focusing on genetic variants described to date that can impact equine foetal viability.
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Affiliation(s)
- Charlotte A Shilton
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Herts, AL9 7TA, UK
| | - Anne Kahler
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Herts, AL9 7TA, UK
| | - Jessica M Roach
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Herts, AL9 7TA, UK
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA
| | - Amanda M de Mestre
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, Herts, AL9 7TA, UK
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Kim HI, Choi EA, Paik EC, Park S, Hwang YI, Lee JH, Seo SK, Cho S, Choi YS, Lee BS, Park J, Lee S, Lee KR, Yun BH. Identification of Single Nucleotide Polymorphisms as Biomarkers for Recurrent Pregnancy Loss in Korean Women. J Korean Med Sci 2022; 37:e336. [PMID: 36631028 PMCID: PMC9705206 DOI: 10.3346/jkms.2022.37.e336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/12/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) are reportedly associated with repeated abortion. Thus, genetic analysis based on race is the key to developing accurate diagnostic tests. This study analyzed the genetic polymorphisms of recurrent pregnancy loss (RPL) patients among Korean women compared to the controls. METHODS In 53 women of RPL group and 50 controls, the genetic analysis was performed. The genotype distribution and allele frequency were analyzed statistically for the difference between the two groups. The association between each SNP marker and RPL risk was analyzed. RESULTS The genotypes of LEPR, endothelial nitric oxide synthase (eNOS), KDR, miR-27a, miR-449b, and tumor necrosis factor-alpha (TNF-α) were analyzed using odds ratio (OR) with 95% confidence intervals (CIs). Only the AG genotype of miR-449b (A>G) polymorphism showed significant association with the risk of RPL when compared to the AA genotype (OR, 2.39). The combination of GG/AG+GG/CA+AA genotypes for eNOS/miR-449b/TNF-α was associated with 7.36-fold higher risk of RPL (OR, 7.36). The GG/AG+GG combination for eNOS/miR-449b showed 2.43-fold higher risk for RPL (OR, 2.43). The combination of AG+GG/CA+AA genotypes for miR-449b/TNF-α showed a significant association with the risk of RPL (OR, 7.60). From the haplotype-based analysis, the G-G-A haplotype of eNOS/miR-449b/TNF-α and the G-A haplotype of miR-449b/TNF-α were associated with increased risk of RPL (OR, 19.31; OR, 22.08, respectively). CONCLUSION There is a significant association between the risk of RPL and miR-449b/TNF-α combination, and therefore, genetic analysis for specific combined genotypes can be an important screening method for RPL in Korean women.
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Affiliation(s)
- Hye In Kim
- Department of Obstetrics and Gynecology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Eun A Choi
- Department of Obstetrics and Gynecology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | | | | | - Yu Im Hwang
- Bundang Cheil Women's Hospital, Seongnam, Korea
| | - Jae Hoon Lee
- Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Seok Kyo Seo
- Department of Obstetrics and Gynecology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - SiHyun Cho
- Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Young Sik Choi
- Department of Obstetrics and Gynecology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Byung Seok Lee
- Department of Obstetrics and Gynecology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Jimyeong Park
- Seoul Clinical Laboratories Healthcare Co., Ltd., Yongin, Korea
| | - Sanghoo Lee
- Seoul Clinical Laboratories Healthcare Co., Ltd., Yongin, Korea.
| | - Kyoung-Ryul Lee
- Seoul Clinical Laboratories Healthcare Co., Ltd., Yongin, Korea
| | - Bo Hyon Yun
- Department of Obstetrics and Gynecology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
- Bundang Cheil Women's Hospital, Seongnam, Korea.
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Chen Y, Yu C, Hu F, Zhu Y, Xie X. Astragalus polysaccharides combined with Codonopsis pilosula polysaccharides modulates the physiological characteristics of trophoblasts via miR-92a-1–5p/CCR7 axis. Tissue Cell 2022; 77:101827. [DOI: 10.1016/j.tice.2022.101827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 11/19/2022]
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Zhang X, Wu H, Gu Z, Yu Z, Lan L, Huang Q. Chromosomal Copy Number Variation Analysis in Pregnancy Products from Recurrent and Sporadic Miscarriage Using Next-Generation Sequencing. Reprod Sci 2022. [PMID: 35578104 DOI: 10.1007/s43032-022-00969-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/07/2022] [Indexed: 10/18/2022]
Abstract
Chromosomal abnormality is one of the causes of fetal miscarriage. The potential differences of fetal chromosomal abnormalities in sporadic miscarriage (SM) and recurrent miscarriage (RM) remain unclear. The purpose of this study was to investigate copy number variations (CNVs) in SM and RM to provide useful genetic guidance for pregnancy and prenatal diagnosis. Four hundred eight samples of aborted fetuses were analyzed by CNV sequencing, and further functional enrichment analysis was performed. Chromosomal abnormalities were identified in 218 (53.4%) fetuses. There were 62 cases (15.2%) with structural chromosomal abnormalities, including 41 with VUS CNVs, 8 with pathogenic CNVs (pCNVs), and 5 with likely pCNVs. Duplications or deletions of 7p22, 8p22, 8p23, and Xp22.31 were significantly more common in RM cases and therefore believed to be related to RM. A total of 289 genes were identified, and 29 different functions were enriched as potential RM candidate genes and functions, which were mainly concentrated in 4 functional categories: chemokines and chemotaxis, protease activity and protein modification, defense response to bacterial and fungal infections, and immune response. The results of this study may improve our understanding of the etiology of RM and contribute to the establishment of a population-based genetic marker information for RM.
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Cheng Z, Cheng D, Li J, Guo L, Zhang W, Zhang C, Liu Y, Huang Y, Xu K. Polymorphisms Within DNA Double-Strand Breaks Repair-Related Genes Contribute to Structural Chromosome Abnormality in Recurrent Pregnancy Loss. Front Genet 2022; 12:787718. [PMID: 35003222 PMCID: PMC8733605 DOI: 10.3389/fgene.2021.787718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/06/2021] [Indexed: 12/05/2022] Open
Abstract
Background: Structural chromosome abnormality (SCA) is an important cause of human diseases, including recurrent pregnancy loss (RPL). DNA double-strand breaks (DSBs) repair-related genes play critical roles in SCA. The present study aims to investigate the potential contribution of DSBs repair-related gene polymorphisms to SCA. Methods: Fifty-four affected RPL individuals with SCA, 88 affected RPL individuals without SCA, and 84 controls were analyzed. Targeted whole-exome sequencing (WES) was used for screening single nucleotide polymorphisms in six DSBs repair-related genes (EP300, XRCC6, LIG4, XRCC4, PRKDC, and DCLRE1C), and validation was performed by Sanger sequencing. Finally, we detected the frequency of radiation-induced chromosome translocations in no SCA samples with significant polymorphisms by fluorescence in situ hybridization (FISH). Results: A total of 35 polymorphisms have been identified and confirmed. Frequencies of EP300 rs20551, XRCC6 rs132788, and LIG4 rs1805388 were significantly different between SCA RPL and no SCA RPL (p = 0.030, 0.031, and 0.040 respectively). Frequencies of those three gene polymorphisms between SCA RPL and controls also were significantly different (p = 0.017, 0.028, and 0.029 respectively). Moreover, the frequency of the G allele at rs20551 locus, the T allele at rs132788 locus and the A allele at rs1805388 locus was significantly higher in SCA RPL than no SCA RPL (OR = 3.227, p = 0.005; OR = 1.978, p = 0.008 and OR = 1.769, p = 0.036 respectively) and controls (OR = 7.130, p = 0.000; OR = 2.157, p = 0.004; OR = 2.397, p = 0.003 respectively). Additionally, the frequency of radiation-induced translocation in no SCA samples with rs20551, rs132788 or rs1805388 was significantly higher compared with the wild type samples (p = 0.015, 0.012, and 0.007 respectively). Conclusion: Our results suggest that rs20551, rs132788, and rs1805388 might be associated with the risk of SCA. Larger scales of genetic variations studies and functional experiments are necessary to further confirm these findings.
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Affiliation(s)
- Zhenbo Cheng
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Dehua Cheng
- School of Basic Medical Science, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Jiancheng Li
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Lihuang Guo
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Wei Zhang
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Conghui Zhang
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yangxu Liu
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yue Huang
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Keqian Xu
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
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Kasak L, Rull K, Yang T, Roden DM, Laan M. Recurrent Pregnancy Loss and Concealed Long-QT Syndrome. J Am Heart Assoc 2021; 10:e021236. [PMID: 34398675 PMCID: PMC8649249 DOI: 10.1161/jaha.121.021236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Recurrent pregnancy loss affects 1% to 2% of couples attempting childbirth. A large fraction of all cases remains idiopathic, which warrants research into monogenic causes of this distressing disorder. Methods and Results We investigated a nonconsanguineous Estonian family who had experienced 5 live births, intersected by 3 early pregnancy losses, and 6 fetal deaths, 3 of which occurred during the second trimester. No fetal malformations were described at the autopsies performed in 3 of 6 cases of fetal death. Parental and fetal chromosomal abnormalities (including submicroscopic) and maternal risk factors were excluded. Material for genetic testing was available from 4 miscarried cases (gestational weeks 11, 14, 17, and 18). Exome sequencing in 3 pregnancy losses and the mother identified no rare variants explicitly shared by the miscarried conceptuses. However, the mother and 2 pregnancy losses carried a heterozygous nonsynonymous variant, resulting in p.Val173Asp (rs199472695) in the ion channel gene KCNQ1. It is expressed not only in heart, where mutations cause type 1 long‐QT syndrome, but also in other tissues, including uterus. The p.Val173Asp variant has been previously identified in a patient with type 1 long‐QT syndrome, but not reported in the Genome Aggregation Database. With heterologous expression in CHO cells, our in vitro electrophysiologic studies indicated that the mutant slowly activating voltage‐gated K+ channel (IKs) is dysfunctional. It showed reduced total activating and deactivating currents (P<0.01), with dramatically positive shift of voltage dependence of activation by ≈10 mV (P<0.05). Conclusions The current study uncovered concealed maternal type 1 long‐QT syndrome as a potential novel cause behind recurrent fetal loss.
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Affiliation(s)
- Laura Kasak
- Institute of Biomedicine and Translational Medicine University of Tartu Estonia
| | - Kristiina Rull
- Institute of Biomedicine and Translational Medicine University of Tartu Estonia.,Women's Clinic Tartu University Hospital Tartu Estonia.,Institute of Clinical Medicine University of Tartu Estonia
| | - Tao Yang
- Departments of Medicine, Pharmacology and Biomedical Informatics Vanderbilt University Medical Center Nashville TN
| | - Dan M Roden
- Departments of Medicine, Pharmacology and Biomedical Informatics Vanderbilt University Medical Center Nashville TN
| | - Maris Laan
- Institute of Biomedicine and Translational Medicine University of Tartu Estonia
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Sheng YR, Hou SY, Hu WT, Wei CY, Liu YK, Liu YY, Jiang L, Xiang JJ, Sun XX, Lei CX, Wang HL, Zhu XY. Characterization of Copy-Number Variations and Possible Candidate Genes in Recurrent Pregnancy Losses. Genes (Basel) 2021; 12:141. [PMID: 33499090 DOI: 10.3390/genes12020141] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/09/2021] [Accepted: 01/19/2021] [Indexed: 12/12/2022] Open
Abstract
It is well established that embryonic chromosomal abnormalities (both in the number of chromosomes and the structure) account for 50% of early pregnancy losses. However, little is known regarding the potential differences in the incidence and distribution of chromosomal abnormalities between patients with sporadic abortion (SA) and recurrent pregnancy loss (RPL), let alone the role of submicroscopic copy-number variations (CNVs) in these cases. The aim of the present study was to systematically evaluate the role of embryonic chromosomal abnormalities and CNVs in the etiology of RPL compared with SA. Over a 3-year period, 1556 fresh products of conception (POCs) from miscarriage specimens were investigated using single nucleotide polymorphism array (SNP-array) and CNV sequencing (CNV-seq) in this study, along with further functional enrichment analysis. Chromosomal abnormalities were identified in 57.52% (895/1556) of all cases. Comparisons of the incidence and distributions of chromosomal abnormalities within the SA group and RPL group and within the different age groups were performed. Moreover, 346 CNVs in 173 cases were identified, including 272 duplications, 2 deletions and 72 duplications along with deletions. Duplications in 16q24.3 and 16p13.3 were significantly more frequent in RPL cases, and thereby considered to be associated with RPL. There were 213 genes and 131 signaling pathways identified as potential RPL candidate genes and signaling pathways, respectively, which were centered primarily on six functional categories. The results of the present study may improve our understanding of the etiologies of RPL and assist in the establishment of a population-based diagnostic panel of genetic markers for screening RPL amongst Chinese women.
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Shaker M, Shalabi T, Gaber KR, Amr K. Association of miRNA-27a and leptin polymorphisms with recurrent pregnancy loss in Egyptian women. Meta Gene 2020; 24:100617. [DOI: 10.1016/j.mgene.2019.100617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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Geng Q, Cui X, Zhang Y, Zhang L, Zhang C, Wang K, Chen J, Zhu Q, Xie J, Xu Z, Liu Y, Zhang M, Ding L, Zhang W, Yang C. Screening of triploid with low-coverage whole-genome sequencing by a single-nucleotide polymorphism-based test in miscarriage tissue. J Assist Reprod Genet 2019; 36:2525-2531. [PMID: 31720905 PMCID: PMC6910887 DOI: 10.1007/s10815-019-01588-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/10/2019] [Indexed: 12/14/2022] Open
Abstract
PURPOSE To establish a single-nucleotide polymorphism-based analysis (SBA) method to identify triploidy in the miscarriage tissue by using low-coverage whole-genome sequencing (LC-WGS). METHODS The method was established by fitting a quadratic curve model by counting the distribution of three heterozygous mutation content intervals. The triploid test result was mainly determined by the opening direction and the axis of symmetry of the quadratic curve, and Z test between the same batch samples was also used for auxiliary judgment. RESULTS Two hundred thirteen diploid samples and 8 triploid samples were used for establishment of the analytical method and 203 unknown samples were used for blind testing. In the blind testing, we found 2 cases positive for triploidy. After chromosome microarray analysis (CMA) and mass spectrometry verification, we found that both samples were true positives. We randomly selected 5 samples from the negative samples for mass spectrometry verification, and the results showed that these samples were all true negatives. CONCLUSIONS Our method achieved accurate detection of triploidy in the miscarriage tissue and has the potential to detect more chromosomal abnormality types such as uniparental disomy (UPD) using a single LC-WGS approach.
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Affiliation(s)
- Qian Geng
- Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Xiaoli Cui
- CheerLand Precision Biomed Co.,Ltd, Shenzhen, Guangdong, China
| | - Yaqi Zhang
- CheerLand Precision Biomed Co.,Ltd, Shenzhen, Guangdong, China
| | - Lijuan Zhang
- CheerLand Precision Biomed Co.,Ltd, Shenzhen, Guangdong, China
| | - Cai Zhang
- CheerLand Precision Biomed Co.,Ltd, Shenzhen, Guangdong, China
| | - Kai Wang
- CheerLand Precision Biomed Co.,Ltd, Shenzhen, Guangdong, China
| | - Jianguo Chen
- CheerLand Precision Biomed Co.,Ltd, Shenzhen, Guangdong, China
| | - Qingyan Zhu
- CheerLand Precision Biomed Co.,Ltd, Shenzhen, Guangdong, China
| | - Jiansheng Xie
- Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Zhiyong Xu
- Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Yang Liu
- Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, China
| | - MengMeng Zhang
- CheerLand Precision Biomed Co.,Ltd, Shenzhen, Guangdong, China
| | - Lijie Ding
- CheerLand Precision Biomed Co.,Ltd, Shenzhen, Guangdong, China
| | - Wenyong Zhang
- Southern University of Science and Technology, Shenzhen, China.,Southern University of Science and Technology-CheerLand Institute of Precision Medicine, Shenzhen, Guangdong Sheng, China
| | - Chuanchun Yang
- CheerLand Precision Biomed Co.,Ltd, Shenzhen, Guangdong, China.
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Kashevarova AA, Skryabin NA, Nikitina TV, Lopatkina ME, Sazhenova EA, Zhigalina DI, Savchenko RR, Lebedev IN. Ontogenetic Pleiotropy of Genes Involved in CNVs in Human Spontaneous Abortions. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419100065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Song J, Wang X, Guo Y, Yang Y, Xu K, Wang T, Sa Y, Yuan L, Jiang H, Guo J, Sun Z. Novel high-coverage targeted metabolomics method (SWATHtoMRM) for exploring follicular fluid metabolome alterations in women with recurrent spontaneous abortion undergoing in vitro fertilization. Sci Rep 2019; 9:10873. [PMID: 31350457 DOI: 10.1038/s41598-019-47370-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 07/16/2019] [Indexed: 12/31/2022] Open
Abstract
The complexity of follicular fluid metabolome presents a significant challenge for qualitative and quantitative metabolite profiling, and for discovering the comprehensive biomarkers. In order to address this challenge, a novel SWATHtoMRM metabolomics method was used for providing broad coverage and excellent quantitative capability to discover the human follicular fluid metabolites related to recurrent spontaneous abortion (RSA) after in vitro fertilization and embryo transfer, and to evaluate their relationship with pregnancy outcome. The follicular fluid samples from the spontaneous abortion group (n = 22) and the control group (n = 22) were analyzed using ultra-performance liquid chromatography high-resolution mass spectrometry. A novel, high-coverage, targeted metabolomics method (SWATH to MRM) and a targeted metabolomics method were used to find and validate the differential metabolites between the two groups. A total of 18 follicular fluid metabolites, including amino acids, cholesterol, vitamins, fatty acids, cholic acid, lysophosphatidylcholine and other metabolites, were identified. In the RSA group, 8 metabolites, namely dehydroepiandrosterone, lysoPC(16:0), lysoPC(18:2), lysoPC(18:1), lysoPC(18:0), lysoPC(20:5), lysoPC(20:4), and lysoPC(20:3), were up-regulated, and 10 metabolites, namely phenylalanine, linoleate, oleic acid, docosahexaenoic acid, lithocholic acid, 25-hydroxyvitamin D3, hydroxycholesterol, 13-hydroxy-alpha-tocopherol, leucine, and tryptophan, were down-regulated. These differential metabolites related to RSA may provide a possible diagnostic basis and therapeutic target for RSA, as well as a scientific basis for elucidating the mechanism of RSA.
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15
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Colley E, Hamilton S, Smith P, Morgan NV, Coomarasamy A, Allen S. Potential genetic causes of miscarriage in euploid pregnancies: a systematic review. Hum Reprod Update 2019; 25:452-472. [PMID: 31150545 DOI: 10.1093/humupd/dmz015] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/07/2019] [Indexed: 12/14/2022] Open
Abstract
Abstract
BACKGROUND
Approximately 50% of pregnancy losses are caused by chromosomal abnormalities, such as aneuploidy. The remainder has an apparent euploid karyotype, but it is plausible that there are cases of pregnancy loss with other genetic aberrations that are not currently routinely detected. Studies investigating the use of exome sequencing and chromosomal microarrays in structurally abnormal pregnancies and developmental disorders have demonstrated their clinical application and/or potential utility in these groups of patients. Similarly, there have been several studies that have sought to identify genes that are potentially causative of, or associated with, spontaneous pregnancy loss, but the evidence has not yet been synthesized.
OBJECTIVE AND RATIONALE
The objective was to identify studies that have recorded monogenic genetic contributions to pregnancy loss in euploid pregnancies, establish evidence for genetic causes of pregnancy loss, identify the limitations of current evidence, and make recommendations for future studies. This evidence is important in considering additional research into Mendelian causes of pregnancy loss and appropriate genetic investigations for couples experiencing recurrent pregnancy loss.
SEARCH METHODS
A systematic review was conducted in MEDLINE (1946 to May 2018) and Embase (1974 to May 2018). The search terms ‘spontaneous abortion’, ‘miscarriage’, ‘pregnancy loss’, or ‘lethal’ were used to identify pregnancy loss terms. These were combined with search terms to identify the genetic contribution including ‘exome’, ‘human genome’, ‘sequencing analysis’, ‘sequencing’, ‘copy number variation’, ‘single-nucleotide polymorphism’, ‘microarray analysis’, and ‘comparative genomic hybridization’. Studies were limited to pregnancy loss up to 20 weeks in humans and excluded if the genetic content included genes that are not lethal in utero, PGD studies, infertility studies, expression studies, aneuploidy with no recurrence risk, methodologies where there is no clinical relevance, and complex genetic studies. The quality of the studies was assessed using a modified version of the Newcastle–Ottawa scale.
OUTCOMES
A total of 50 studies were identified and categorized into three themes: whole-exome sequencing studies; copy number variation studies; and other studies related to pregnancy loss including recurrent molar pregnancies, epigenetics, and mitochondrial DNA aberrations. Putatively causative variants were found in a range of genes, including CHRNA1 (cholinergic receptor, nicotinic, alpha polypeptide 1), DYNC2H1 (dynein, cytoplasmic 2, heavy chain 1), and RYR1 (ryanodine receptor 1), which were identified in multiple studies. Copy number variants were also identified to have a causal or associated link with recurrent miscarriage.
WIDER IMPLICATIONS
Identification of genes that are causative of or predisposing to pregnancy loss will be of significant individual patient impact with respect to counselling and treatment. In addition, knowledge of specific genes that contribute to pregnancy loss could also be of importance in designing a diagnostic sequencing panel for patients with recurrent pregnancy loss and also in understanding the biological pathways that can cause pregnancy loss.
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Affiliation(s)
- Emily Colley
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Susan Hamilton
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s Hospital, Birmingham, UK
| | - Paul Smith
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Neil V Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Arri Coomarasamy
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Stephanie Allen
- Tommy’s National Centre for Miscarriage Research, Birmingham Women’s and Children’s Hospital, Birmingham, UK
- West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s Hospital, Birmingham, UK
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Qi H, Xuan ZL, Du Y, Cai LR, Zhang H, Wen XH, Kong XD, Yang K, Mi Y, Fu XX, Cao SB, Wang J, Chen CJ, Liang JB. High resolution global chromosomal aberrations from spontaneous miscarriages revealed by low coverage whole genome sequencing. Eur J Obstet Gynecol Reprod Biol 2018; 224:21-8. [PMID: 29525519 DOI: 10.1016/j.ejogrb.2018.03.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVE Chromosome aberrations are generally considered as one of the most substantial causative factors contributing to spontaneous miscarriages. Cytogenetic analyses like G-banded karyotype and chromosomal microarray analyses are often performed to further investigate the chromosome status of a miscarried fetus. STUDY DESIGN Here, we describe a novel method, AnnoCNV, to detect DNA copy number variations (CNVs) using low coverage whole genome sequencing (WGS). We investigated the overall frequency of chromosomal abnormalities in 149 miscarriage specimens using AnnoCNV. RESULTS Among 149 fetal miscarriage samples, more than two fifths of them (42.95%, 64) carried at least one chromosomal abnormality, and a subset (40) was identified as autosomal trisomy which account for 26.84% of all samples. We have also developed a robust algorithm in AnnoCNV, which is able to differentiate specifically karyotype 69,XXY from sex chromosomal aneuploidy 45,X, and to identify 45,X/46,XX mosaicism. Lastly, across the whole genome AnnoCNV identifies CNVs, which are associated with both reported symptoms and unknown clinical conditions. CONCLUSION This cost-effective strategy reveals genome wide discovery of chromosome aberrations at higher resolution, which are consistent with parallel investigation conducted by SNP based assay.
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17
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Wang NF, Kolte AM, Larsen EC, Nielsen HS, Christiansen OB. Immunologic Abnormalities, Treatments, and Recurrent Pregnancy Loss: What Is Real and What Is Not? Clin Obstet Gynecol 2016; 59:509-23. [PMID: 27380207 DOI: 10.1097/GRF.0000000000000215] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recurrent pregnancy loss, depending on the definition, affects 1% to 3% of women aiming to have a child. Little is known about the direct causes of recurrent pregnancy loss, and the condition is considered to have a multifactorial and complex pathogenesis. The aim of this review was to summarize the evaluation and the management of the condition with specific emphasis on immunologic biomarkers identified as risk factors as well as current immunologic treatment options. The review also highlights and discusses areas in need of further research.
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18
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Karim S, Jamal HS, Rouzi A, Ardawi MSM, Schulten HJ, Mirza Z, Alansari NA, Al-Quaiti MM, Abusamra H, Naseer MI, Turki R, Chaudhary AG, Gari M, Abuzenadah AM, Al-Qhatani MH. Genomic answers for recurrent spontaneous abortion in Saudi Arabia: An array comparative genomic hybridization approach. Reprod Biol 2017; 17:133-143. [DOI: 10.1016/j.repbio.2017.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 03/14/2017] [Accepted: 03/17/2017] [Indexed: 12/29/2022]
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19
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Kasak L, Rull K, Sõber S, Laan M. Copy number variation profile in the placental and parental genomes of recurrent pregnancy loss families. Sci Rep 2017; 7:45327. [PMID: 28345611 PMCID: PMC5366903 DOI: 10.1038/srep45327] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/23/2017] [Indexed: 12/25/2022] Open
Abstract
We have previously shown an extensive load of somatic copy number variations (CNVs) in the human placental genome with the highest fraction detected in normal term pregnancies. Hereby, we hypothesized that insufficient promotion of CNVs may impair placental development and lead to recurrent pregnancy loss (RPL). RPL affects ~3% of couples aiming at childbirth and idiopathic RPL represents ~50% of cases. We analysed placental and parental CNV profiles of idiopathic RPL trios (mother-father-placenta) and duos (mother-placenta). Consistent with the hypothesis, the placental genomes of RPL cases exhibited 2-fold less CNVs compared to uncomplicated 1st trimester pregnancies (P = 0.02). This difference mainly arose from lower number of duplications. Overall, 1st trimester control placentas shared only 5.3% of identified CNV regions with RPL cases, whereas the respective fraction with term placentas was 35.1% (P = 1.1 × 10−9). Disruption of the genes NUP98 (embryonic stem cell development) and MTRR (folate metabolism) was detected exclusively in RPL placentas, potentially indicative to novel loci implicated in RPL. Interestingly, genes with higher overall expression were prone to deletions (>3-fold higher median expression compared to genes unaffected by CNVs, P = 6.69 × 10−20). Additionally, large pericentromeric and subtelomeric CNVs in parental genomes emerged as a risk factor for RPL.
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Affiliation(s)
- Laura Kasak
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia 23 St., Tartu 51010, Estonia
| | - Kristiina Rull
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia 23 St., Tartu 51010, Estonia.,Department of Obstetrics and Gynaecology, University of Tartu, Puusepa St. 8, Tartu 51014, Estonia.,Women's Clinic of Tartu University Hospital, Puusepa St. 8, Tartu 51014, Estonia
| | - Siim Sõber
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia 23 St., Tartu 51010, Estonia.,Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 19, Tartu 51014, Estonia
| | - Maris Laan
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia 23 St., Tartu 51010, Estonia.,Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 19, Tartu 51014, Estonia
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20
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Sõber S, Rull K, Reiman M, Ilisson P, Mattila P, Laan M. RNA sequencing of chorionic villi from recurrent pregnancy loss patients reveals impaired function of basic nuclear and cellular machinery. Sci Rep 2016; 6:38439. [PMID: 27929073 PMCID: PMC5143936 DOI: 10.1038/srep38439] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/08/2016] [Indexed: 12/14/2022] Open
Abstract
Recurrent pregnancy loss (RPL) concerns ~3% of couples aiming at childbirth. In the current study, transcriptomes and miRNomes of 1st trimester placental chorionic villi were analysed for 2 RPL cases (≥6 miscarriages) and normal, but electively terminated pregnancies (ETP; n = 8). Sequencing was performed on Illumina HiSeq 2000 platform. Differential expression analyses detected 51 (27%) transcripts with increased and 138 (73%) with decreased expression in RPL compared to ETP (DESeq: FDR P < 0.1 and DESeq2: <0.05). RPL samples had substantially decreased transcript levels of histones, regulatory RNAs and genes involved in telomere, spliceosome, ribosomal, mitochondrial and intra-cellular signalling functions. Downregulated expression of HIST1H1B and HIST1H4A (Wilcoxon test, fc≤0.372, P≤9.37 × 10−4) was validated in an extended sample by quantitative PCR (RPL, n = 14; ETP, n = 24). Several upregulated genes are linked to placental function and pregnancy complications: ATF4, C3, PHLDA2, GPX4, ICAM1, SLC16A2. Analysis of the miRNA-Seq dataset identified no large disturbances in RPL samples. Notably, nearly 2/3 of differentially expressed genes have binding sites for E2F transcription factors, coordinating mammalian endocycle and placental development. For a conceptus destined to miscarriage, the E2F TF-family represents a potential key coordinator in reprogramming the placental genome towards gradually stopping the maintenance of basic nuclear and cellular functions.
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Affiliation(s)
- Siim Sõber
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, 51010 Tartu, Estonia
| | - Kristiina Rull
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, 51010 Tartu, Estonia.,Department of Obstetrics and Gynaecology, University of Tartu, L. Puusepa St. 8, Tartu 51014, Estonia.,Women's Clinic of Tartu University Hospital, L. Puusepa St. 8, Tartu 51014, Estonia
| | - Mario Reiman
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, 51010 Tartu, Estonia
| | - Piret Ilisson
- Department of Genetics, United Laboratories of Tartu University Hospital, L. Puusepa St. 2, Tartu 51014, Estonia
| | - Pirkko Mattila
- The Institute for Molecular Medicine Finland (FIMM), Tukholmankatu 8, Helsinki FI-00014 Finland.,Finnish Red Cross Blood Service (FRCBS), Kivihaantie 7, Helsinki FI-00310, Finland
| | - Maris Laan
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, 51010 Tartu, Estonia.,Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 19, 50412 Tartu, Estonia
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21
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Xi R, Lee S, Xia Y, Kim TM, Park PJ. Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants. Nucleic Acids Res 2016; 44:6274-86. [PMID: 27260798 PMCID: PMC5772337 DOI: 10.1093/nar/gkw491] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/22/2016] [Indexed: 12/16/2022] Open
Abstract
Whole-genome sequencing data allow detection of copy number variation (CNV) at high resolution. However, estimation based on read coverage along the genome suffers from bias due to GC content and other factors. Here, we develop an algorithm called BIC-seq2 that combines normalization of the data at the nucleotide level and Bayesian information criterion-based segmentation to detect both somatic and germline CNVs accurately. Analysis of simulation data showed that this method outperforms existing methods. We apply this algorithm to low coverage whole-genome sequencing data from peripheral blood of nearly a thousand patients across eleven cancer types in The Cancer Genome Atlas (TCGA) to identify cancer-predisposing CNV regions. We confirm known regions and discover new ones including those covering KMT2C, GOLPH3, ERBB2 and PLAG1. Analysis of colorectal cancer genomes in particular reveals novel recurrent CNVs including deletions at two chromatin-remodeling genes RERE and NPM2. This method will be useful to many researchers interested in profiling CNVs from whole-genome sequencing data.
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Affiliation(s)
- Ruibin Xi
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing 100871, China
| | - Semin Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Yuchao Xia
- School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing 100871, China Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Tae-Min Kim
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, 137-701 Seoul, Korea
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
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22
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Markoff A, Kurahashi H, Grandone E, Bogdanova N. Annexin A5 haplotype M2 is not a risk factor for recurrent spontaneous abortion in Northern Europe: is there sufficient evidence? Reprod Biomed Online 2016; 32:469-73. [PMID: 26966050 DOI: 10.1016/j.rbmo.2016.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/29/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
Abstract
The M2 haplotype of the annexin A5 gene is a well-recognized predisposition factor for recurrent spontaneous abortion (RSA). A recent publication by Nagirnaja et al. (2015) in PLoS One discusses the risk role of the M2 haplotype for RSA in cases compared with controls of North European extraction and arrives at a negative result. As a number of previous and fairly recent studies have supported the proposed involvement of the M2 haplotype in the cause of idiopathic RSA, this commentary aims to highlight problematic issues in the above publication. It is the opinion of the authors that the study by Nagirnaja et al. (2015) does not generate adequate proof of the absence of RSA risk, attributable to carriage of the M2 haplotype.
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Affiliation(s)
- Arseni Markoff
- Institute of Human Genetics, University of Muenster, Vesaliusweg 12-14, 48149 Muenster, Germany.
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Elvira Grandone
- Atherosclerosis and Thrombosis Unit, I.R.C.C.S. "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Foggia 71013, Italy
| | - Nadja Bogdanova
- Institute of Human Genetics, University of Muenster, Vesaliusweg 12-14, 48149 Muenster, Germany
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23
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Qiao Y, Wen J, Tang F, Martell S, Shomer N, Leung PCK, Stephenson MD, Rajcan-Separovic E. Whole exome sequencing in recurrent early pregnancy loss. Mol Hum Reprod 2016; 22:364-72. [PMID: 26826164 DOI: 10.1093/molehr/gaw008] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/25/2016] [Indexed: 12/20/2022] Open
Abstract
STUDY HYPOTHESIS Exome sequencing can identify genetic causes of idiopathic recurrent pregnancy loss (RPL). STUDY FINDING We identified compound heterozygous deleterious mutations affecting DYNC2H1 and ALOX15 in two out of four families with RPL. Both genes have a role in early development. Bioinformatics analysis of all genes with rare and putatively pathogenic mutations in miscarriages and couples showed enrichment in pathways relevant to pregnancy loss, including the complement and coagulation cascades pathways. WHAT IS KNOWN ALREADY Next generation sequencing (NGS) is increasingly being used to identify known and novel gene mutations in children with developmental delay and in fetuses with ultrasound-detected anomalies. In contrast, NGS is rarely used to study pregnancy loss. Chromosome microarray analysis detects putatively causative DNA copy number variants (CNVs) in ∼2% of miscarriages and CNVs of unknown significance (predominantly parental in origin) in up to 40% of miscarriages. Therefore, a large number of miscarriages still have an unknown cause. STUDY DESIGN, SAMPLES/MATERIALS, METHODS Whole exome sequencing (WES) was performed using Illumina HiSeq 2000 platform on seven euploid miscarriages from four families with RPL. Golden Helix SVS v8.1.5 was used for data assessment and inheritance analysis for deleterious DNA variants predicted to severely disrupt protein-coding genes by introducing a frameshift, loss of the stop codon, gain of the stop codon, changes in splicing or the initial codon. Webgestalt (http://bioinfo.vanderbilt.edu/webgestalt/) was used for pathway and disease association enrichment analysis of a gene pool containing putatively pathogenic variants in miscarriages and couples in comparison to control gene pools. MAIN RESULTS AND THE ROLE OF CHANCE Compound heterozygous mutations in DYNC2H1 and ALOX15 were identified in miscarriages from two families with RPL. DYNC2H1 is involved in cilia biogenesis and has been associated with fetal lethality in humans. ALOX15 is expressed in placenta and its dysregulation has been associated with inflammation, placental, dysfunction, abnormal oxidative stress response and angiogenesis. The pool of putatively pathogenic single nucleotide variants (SNVs) and small insertions and deletions (indels) detected in the miscarriages showed enrichment in 'complement and coagulation cascades pathway', and 'ciliary motility disorders'. We conclude that CNVs, individual SNVs and pool of deleterious gene mutations identified by exome sequencing could contribute to RPL. LIMITATIONS, REASONS FOR CAUTION The size of our sample cohort is small. The functional effect of candidate mutations should be evaluated to determine whether the mutations are causative. WIDER IMPLICATIONS OF THE FINDINGS This is the first study to assess whether SNVs may contribute to the pathogenesis of miscarriage. Furthermore, our findings suggest that collective effect of mutations in relevant biological pathways could be implicated in RPL. STUDY FUNDING AND COMPETING INTERESTS The study was funded by Canadian Institutes of Health Research (grant MOP 106467) and Michael Smith Foundation of Health Research Career Scholar salary award to ERS.
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Affiliation(s)
- Ying Qiao
- Department of Pathology, BC Child and Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC, Canada
| | - Jiadi Wen
- University of Texas, Dallas, TX, USA
| | - Flamingo Tang
- Department of Pathology, BC Child and Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC, Canada
| | - Sally Martell
- Department of Pathology, BC Child and Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC, Canada
| | - Naomi Shomer
- Department of Pathology, BC Child and Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC, Canada
| | - Peter C K Leung
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada V6Z 2 K5
| | - Mary D Stephenson
- University of Chicago and University of Illinois at Chicago, Chicago, IL, USA
| | - Evica Rajcan-Separovic
- Department of Pathology, BC Child and Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC, Canada
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Nagirnaja L, Nõmmemees D, Rull K, Christiansen OB, Nielsen HS, Laan M. Annexin A5 Promoter Haplotype M2 Is Not a Risk Factor for Recurrent Pregnancy Loss in Northern Europe. PLoS One 2015; 10:e0131606. [PMID: 26135579 DOI: 10.1371/journal.pone.0131606] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 06/03/2015] [Indexed: 12/16/2022] Open
Abstract
Introduction Annexin A5 is an essential component of placental integrity that may potentially mediate susceptibility to phenotypes of compromised pregnancy. A promoter haplotype termed M2 of the coding gene ANXA5 has been implicated in various pregnancy complications such as preeclampsia and recurrent pregnancy loss (RPL), however with inconclusive results. Study subjects and methods A retrospective case-control study combining resequencing and restriction fragment length polymorphism (RFLP) analysis was undertaken in 313 women with unexplained RPL and 214 fertile women from Estonia and Denmark to estimate the RPL disease risk of the M2 haplotype in Northern Europe. Comparative prevalence of the studied ANXA5 genetic variants in human populations was estimated based on the 1000 Genomes Project (n = 675, whole-genome sequencing data) and the KORA S3 500K dataset of South German samples (n = 1644, genome-wide genotyping data). Results Minor allele frequency of common polymorphisms in ANXA5 promoter was up to two-fold lower among Estonian RPL subjects than fertile controls. The M2 haplotype was not associated with RPL and a trend for decreased prevalence was observed among RPL patients compared to controls both in Estonia (8.1% vs 15.2%, respectively) and Denmark (9.7% vs 12.6%). The high M2 prevalence in fertile controls was consistent with estimations for European and East Asian populations (9.6%-16.0%). Conclusions This study cautions to consider the M2 haplotype as a deterministic factor in early pregnancy success because: i) no RPL disease risk was associated with the haplotype in two clinically well-characterized RPL case-control study samples, ii) high prevalence of the haplotype among fertile controls and world-wide populations is inconsistent with the previously proposed severe impact on early pregnancy success, iii) weak impact of M2 haplotype on the production of ANXA5 protein has been established by others.
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Bagheri H, Mercier E, Qiao Y, Stephenson MD, Rajcan-Separovic E. Genomic characteristics of miscarriage copy number variants. Mol Hum Reprod 2015; 21:655-61. [PMID: 26071097 DOI: 10.1093/molehr/gav030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/09/2015] [Indexed: 01/08/2023] Open
Abstract
Studies of copy number variants (CNVs) in miscarriages are rare in comparison to post-natal cases with developmental abnormalities. The overall characteristics of miscarriage CNVs (size, gene content and function) are therefore largely unexplored. Our goal was to assess and compare the characteristics of CNVs identified in 101 euploid miscarriages from four high-resolution array studies that documented both common miscarriage CNVs (i.e. CNVs found in controls from the Database of Genomic Variants, DGV) and rare miscarriage CNVs (not reported in DGV). Our miscarriage analysis included 24 rare CNVs with 93 genes, and 372 common CNVs (merged into 119 common CNV regions; CNVRs) with 354 genes. The rare and common CNVs were comparable in size (median size of ∼ 0.16 and 0.14 Mb, respectively); however, rare CNVs showed a significantly higher gene density, with 56 genes/Mb in rare and 24 genes/Mb in common CNVs (P = 0.03). Rare CNVs also had two times more genes with mouse knock-out models which were reported for 42% of rare and 19% of common CNV genes. No specific pathway enrichment was noted for 24 rare CNV genes, but common CNV genes showed significant enrichment in genes from immune-response related pathways and pregnancy/reproduction-related biological processes. Our analysis of CNVs from euploid miscarriages suggests that both rare and common CNVs could have a role in miscarriage by impacting pregnancy-related genes or pathways. Cataloguing of all CNVs and detailed description of their characteristics (e.g. gene content, genomic breakpoints) is desirable in the future for better understanding of their relevance to pregnancy loss.
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Affiliation(s)
- Hani Bagheri
- Department of Pathology and Laboratory Medicine, BC Child and Family Research Institute, University of British Columbia (UBC), Vancouver, BC V5Z 4H4, Canada
| | | | - Ying Qiao
- Department of Pathology and Laboratory Medicine, BC Child and Family Research Institute, University of British Columbia (UBC), Vancouver, BC V5Z 4H4, Canada
| | - Mary D Stephenson
- Department of Obstetrics and Gynaecology, University of Illinois at Chicago, Chicago, IL, USA
| | - Evica Rajcan-Separovic
- Department of Pathology and Laboratory Medicine, BC Child and Family Research Institute, University of British Columbia (UBC), Vancouver, BC V5Z 4H4, Canada
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Abstract
Placenta is a temporary, but indispensable organ in mammalian pregnancy. From its basic nature, it exhibits highly invasive tumour-like properties facilitating effective implantation through trophoblast cell proliferation and migration, and a critical role in pregnancy success. We hypothesized that similarly to cancer, somatic genomic rearrangements are promoted in the support of placental function. Here we present the first profiling of copy number variations (CNVs) in human placental genomes, showing an extensive load of somatic CNVs, especially duplications and suggesting that this phenomenon may be critical for normal gestation. Placental somatic CNVs were significantly enriched in genes involved in cell adhesion, immunity, embryonic development and cell cycle. Overrepresentation of imprinted genes in somatic duplications suggests that amplified gene copies may represent an alternative mechanism to support parent-of-origin specific gene expression. Placentas from pregnancy complications exhibited significantly altered CNV profile compared to normal gestations, indicative to the clinical implications of the study.
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Affiliation(s)
- Laura Kasak
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia
| | - Kristiina Rull
- 1] Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia [2] Department of Obstetrics and Gynaecology, University of Tartu, Puusepa St. 8, Tartu 51014, Estonia [3] Women's Clinic of Tartu University Hospital, Puusepa St. 8, Tartu 51014, Estonia
| | - Pille Vaas
- 1] Department of Obstetrics and Gynaecology, University of Tartu, Puusepa St. 8, Tartu 51014, Estonia [2] Women's Clinic of Tartu University Hospital, Puusepa St. 8, Tartu 51014, Estonia
| | - Pille Teesalu
- 1] Department of Obstetrics and Gynaecology, University of Tartu, Puusepa St. 8, Tartu 51014, Estonia [2] Women's Clinic of Tartu University Hospital, Puusepa St. 8, Tartu 51014, Estonia
| | - Maris Laan
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Riia St. 23, Tartu 51010, Estonia
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Wen J, Hanna CW, Martell S, Leung PC, Lewis SM, Robinson WP, Stephenson MD, Rajcan-Separovic E. Functional consequences of copy number variants in miscarriage. Mol Cytogenet 2015; 8:6. [PMID: 25674159 PMCID: PMC4324423 DOI: 10.1186/s13039-015-0109-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 01/09/2015] [Indexed: 02/01/2023] Open
Abstract
Background The presence of unique copy number variations (CNVs) in miscarriages suggests that their integral genes have a role in maintaining early pregnancy. In our previous work, we identified 19 unique CNVs in ~40% of studied euploid miscarriages, which were predominantly familial in origin. In our current work, we assessed their relevance to miscarriage by expression analysis of 14 genes integral to CNVs in available miscarriage chorionic villi. As familial CNVs could cause miscarriage due to imprinting effect, we investigated the allelic expression of one of the genes (TIMP2) previously suggested to be maternally expressed in placenta and involved in placental remodelling and embryo development. Results Six out of fourteen genes had detectable expression in villi and for three genes the RNA and protein expression was altered due to maternal CNVs. These genes were integral to duplication on Xp22.2 (TRAPPC2 and OFD1) or disrupted by a duplication mapping to 17q25.3 (TIMP2). RNA and protein expression was increased for TRAPPC2 and OFD1 and reduced for TIMP2 in carrier miscarriages. The three genes have roles in processes important for pregnancy development such as extracellular matrix homeostasis (TIMP2 and TRAPPC2) and cilia function (OFD1). TIMP2 allelic expression was not affected by the CNV in miscarriages in comparison to control elective terminations. Conclusion We propose that functional studies of CNVs could help determine if and how the miscarriage CNVs affect the expression of integral genes. In case of parental CNVs, assessment of the function of their integral genes in parental reproductive tissues should be also considered in the future, especially if they affect processes relevant for pregnancy development and support. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0109-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiadi Wen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, V6T 2B5 Canada.,Child & Family Research Institute, Vancouver, V5Z 4H4 Canada
| | - Courtney W Hanna
- Child & Family Research Institute, Vancouver, V5Z 4H4 Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z3 Canada
| | - Sally Martell
- Child & Family Research Institute, Vancouver, V5Z 4H4 Canada
| | - Peter Ck Leung
- Child & Family Research Institute, Vancouver, V5Z 4H4 Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, V6Z 2 K5 Canada
| | - Suzanne Me Lewis
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z3 Canada
| | - Wendy P Robinson
- Child & Family Research Institute, Vancouver, V5Z 4H4 Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z3 Canada
| | - Mary D Stephenson
- Department of Obstetrics and Gynecology, University of Illinois at Chicago, Chicago, 60612 USA
| | - Evica Rajcan-Separovic
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, V6T 2B5 Canada.,Child & Family Research Institute, Vancouver, V5Z 4H4 Canada
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